3GQ8 | pdb_00003gq8

Crystal Structure of the Bacteriophage phi29 gene product 12 N-terminal fragment in complex with 2-(N-cyclohexylamino)ethane sulfonic acid (CHES)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GQ7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	10	298	100mM CHES at ~pH 10.0 and 8% PEG3K, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.62	66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.841	α = 90
b = 90.841	β = 90
c = 586.952	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2008-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.03	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2	44.24	98.3	0.103	25.233	10.6		62712

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	100		0.447		11.2	6289

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3GQ7	2	44.24	62691	3179	98.16	0.17	0.169	0.17	0.196	0.2	RANDOM	23.901

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
1.16	0.58		1.16		-1.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.391
r_dihedral_angle_4_deg	17.072
r_dihedral_angle_3_deg	13.214
r_dihedral_angle_1_deg	6.704
r_scangle_it	3.127
r_scbond_it	2.014
r_angle_refined_deg	1.279
r_mcangle_it	1.118
r_mcbond_it	0.675
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.391
r_dihedral_angle_4_deg	17.072
r_dihedral_angle_3_deg	13.214
r_dihedral_angle_1_deg	6.704
r_scangle_it	3.127
r_scbond_it	2.014
r_angle_refined_deg	1.279
r_mcangle_it	1.118
r_mcbond_it	0.675
r_nbtor_refined	0.304
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.185
r_symmetry_hbond_refined	0.175
r_metal_ion_refined	0.12
r_xyhbond_nbd_refined	0.109
r_chiral_restr	0.097
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4478
Nucleic Acid Atoms
Solvent Atoms	303
Heterogen Atoms	23

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.